SMTL ID : 2a3w.1 (1 other biounit)

Decameric structure of human serum amyloid P-component bound to Bis-1,2-{[(Z)-2-carboxy-2-methyl-1,3-dioxane]-5-yloxycarbamoyl}-ethane

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-10-mer

Ligands

20 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: E.136, D.138, Q.148 Ligands: CA.2, CPJ.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.136, A:D.138, A:D.138, H2O.1, H2O.1 CA.2: 7 residues within 4Å: Chain A: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.1, CPJ.3 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.58, A:D.58, A:E.136, A:Q.137, A:D.138 CA.4: 5 residues within 4Å: Chain B: E.136, D.138, Q.148 Ligands: CA.5, CPJ.6 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.136, B:D.138, B:D.138, H2O.8, H2O.9 CA.5: 7 residues within 4Å: Chain B: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.4, CPJ.6 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.58, B:E.136, B:E.136, B:Q.137, B:D.138 CA.7: 7 residues within 4Å: Chain C: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.8, CPJ.9 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.58, C:E.136, C:E.136, C:Q.137, C:D.138 CA.8: 5 residues within 4Å: Chain C: E.136, D.138, Q.148 Ligands: CA.7, CPJ.9 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.136, C:D.138, C:D.138, H2O.14, H2O.14 CA.10: 7 residues within 4Å: Chain D: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.11, CPJ.12 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.58, D:E.136, D:E.136, D:Q.137, D:D.138 CA.11: 5 residues within 4Å: Chain D: E.136, D.138, Q.148 Ligands: CA.10, CPJ.12 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.136, D:D.138, D:D.138, H2O.20, H2O.20 CA.13: 7 residues within 4Å: Chain E: D.58, N.59, E.136, Q.137, D.138 Ligands: CA.14, CPJ.15 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.58, E:D.58, E:E.136, E:Q.137, E:D.138 CA.14: 5 residues within 4Å: Chain E: E.136, D.138, Q.148 Ligands: CA.13, CPJ.15 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.136, E:D.138, E:D.138, H2O.25, H2O.25 CA.16: 5 residues within 4Å: Chain F: E.136, D.138, Q.148 Ligands: CPJ.15, CA.17 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.136, F:D.138, F:D.138, H2O.31, H2O.31 CA.17: 7 residues within 4Å: Chain F: D.58, N.59, E.136, Q.137, D.138 Ligands: CPJ.15, CA.16 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.58, F:E.136, F:E.136, F:Q.137, F:D.138 CA.18: 7 residues within 4Å: Chain G: D.58, N.59, E.136, Q.137, D.138 Ligands: CPJ.12, CA.19 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.58, G:E.136, G:E.136, G:Q.137, G:D.138 CA.19: 5 residues within 4Å: Chain G: E.136, D.138, Q.148 Ligands: CPJ.12, CA.18 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:E.136, G:D.138, G:D.138, H2O.36, H2O.36 CA.20: 7 residues within 4Å: Chain H: D.58, N.59, E.136, Q.137, D.138 Ligands: CPJ.9, CA.21 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:D.58, H:D.58, H:E.136, H:E.136, H:D.138 CA.21: 5 residues within 4Å: Chain H: E.136, D.138, Q.148 Ligands: CPJ.9, CA.20 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:E.136, H:D.138, H:D.138, H2O.41, H2O.41 CA.22: 7 residues within 4Å: Chain I: D.58, N.59, E.136, Q.137, D.138 Ligands: CPJ.6, CA.23 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:D.58, I:E.136, I:E.136, I:Q.137, I:D.138 CA.23: 5 residues within 4Å: Chain I: E.136, D.138, Q.148 Ligands: CPJ.6, CA.22 5 PLIP interactions: 3 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:E.136, I:D.138, I:D.138, H2O.46, H2O.46 CA.24: 5 residues within 4Å: Chain J: E.136, D.138, Q.148 Ligands: CPJ.3, CA.25 5 PLIP interactions: 3 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:E.136, J:D.138, J:D.138, H2O.51, H2O.51 CA.25: 7 residues within 4Å: Chain J: D.58, N.59, E.136, Q.137, D.138 Ligands: CPJ.3, CA.24 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:D.58, J:E.136, J:E.136, J:Q.137, J:D.138

5 x CPJ: BIS-1,2-{[(Z)-2-CARBOXY-2-METHYL-1,3-DIOXANE]-5-YLOXYCARBAMOYL}-ETHANE(Non-covalent)

CPJ.3: 18 residues within 4Å: Chain A: D.58, N.59, L.62, Y.74, E.136, D.138, Q.148 Chain J: D.58, N.59, L.62, Y.74, E.136, D.138, Q.148 Ligands: CA.1, CA.2, CA.24, CA.25 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain J Hydrophobic interactions: A:L.62, J:L.62 Hydrogen bonds: A:N.59, A:Q.148, J:N.59, J:N.59, J:Q.148 CPJ.6: 19 residues within 4Å: Chain B: D.58, N.59, L.62, Y.74, E.136, D.138, Q.148 Chain I: D.58, N.59, L.62, Y.64, Y.74, E.136, D.138, Q.148 Ligands: CA.4, CA.5, CA.22, CA.23 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain I Hydrophobic interactions: B:L.62, I:L.62, I:Y.64 Hydrogen bonds: B:Q.148, I:N.59, I:N.59, I:Q.148 CPJ.9: 19 residues within 4Å: Chain C: D.58, N.59, L.62, Y.74, E.136, D.138, Q.148 Chain H: D.58, N.59, L.62, Y.64, Y.74, E.136, D.138, Q.148 Ligands: CA.7, CA.8, CA.20, CA.21 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain H Hydrophobic interactions: C:L.62, H:L.62, H:Y.64 Hydrogen bonds: C:N.59, C:Q.148, H:N.59, H:N.59, H:Q.148 Water bridges: H:D.58 CPJ.12: 19 residues within 4Å: Chain D: D.58, N.59, L.62, Y.74, E.136, D.138, Q.148 Chain G: D.58, N.59, L.62, Y.64, Y.74, E.136, D.138, Q.148 Ligands: CA.10, CA.11, CA.18, CA.19 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain G Hydrophobic interactions: D:L.62, G:L.62 Hydrogen bonds: D:N.59, D:Q.148, G:N.59, G:N.59, G:Q.148 CPJ.15: 19 residues within 4Å: Chain E: D.58, N.59, L.62, Y.74, E.136, D.138, Q.148 Chain F: D.58, N.59, L.62, Y.64, Y.74, E.136, D.138, Q.148 Ligands: CA.13, CA.14, CA.16, CA.17 9 PLIP interactions: 3 interactions with chain E, 6 interactions with chain F Hydrophobic interactions: E:L.62, F:L.62 Hydrogen bonds: E:N.59, E:Q.148, F:N.59, F:N.59, F:Q.148 Water bridges: F:D.58, F:D.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ho, J.G. et al., Ligand-assisted Aggregation of Proteins: DIMERIZATION OF SERUM AMYLOID P COMPONENT BY BIVALENT LIGANDS. J.Biol.Chem. (2005)

Release Date

2005-07-26

Peptides

Serum amyloid P-component: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

Serum amyloid P-component

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